K. Bahar Halpern

The cellular states and fates of shed intestinal cells

This study uses RNA sequencing of mouse fecal washes to show shed intestinal cells remain viable and up-regulate anti-microbial programs, and identifies immune cell shedding in colitis.

The spatio-temporal program of liver zonal regeneration

This study uses spatially-resolved single-cell RNA sequencing to analyze mouse liver regeneration after acetaminophen intoxication, revealing zonal dynamics and cell-type-specific responses.

Spatial expression programs of the intestinal follicle-associated epithelium

The paper maps spatial gene expression in intestinal follicle-associated epithelium using RNA sequencing and imaging, revealing zonated expression patterns and distinct cell states.

Clump sequencing exposes the spatial expression programs of intestinal secretory cells

ClumpSeq reconstructs spatial atlases of rare intestinal cell types by sequencing small clumps of attached cells and inferring their position along the crypt-villus axis.

Lgr5+ telocytes are a signaling hub at the intestinal villus tip

The paper identifies Lgr5+ telocytes at the intestinal villus tip as signaling hubs that regulate epithelial gene zonation through Bmp and Wnt5a signals.